Hi,
I'm trying to do some quality scoring/trimming on some Illumina, SE RNAseq data, but keep getting an unusual error message from Fastx. The reads are 36bp long, and I suspect that these use the older Illumina quality scores instead of today's ASCII-33, which may be the problem.
Here is the command and its output:
fastx_quality_stats -Q33 -i myInput.fastq -o myOutput.fastq.stats
fastx_quality_stats: Invalid input: expecting FASTQ prefix character '@' on line 32868957. Is this a valid FASTQ file?
This line in question is the last line of the file. I tried paring back the read file to make sure the last read wasn't truncated or something, but I still get the same error.
If I run the command without the "-Q33" I get the following:
fastx_quality_stats: Invalid quality score value (char '#' ord 35 quality value -29) on line 4
I'm eager to try suggestions, so please let me know ! thanks
I'm trying to do some quality scoring/trimming on some Illumina, SE RNAseq data, but keep getting an unusual error message from Fastx. The reads are 36bp long, and I suspect that these use the older Illumina quality scores instead of today's ASCII-33, which may be the problem.
Here is the command and its output:
fastx_quality_stats -Q33 -i myInput.fastq -o myOutput.fastq.stats
fastx_quality_stats: Invalid input: expecting FASTQ prefix character '@' on line 32868957. Is this a valid FASTQ file?
This line in question is the last line of the file. I tried paring back the read file to make sure the last read wasn't truncated or something, but I still get the same error.
If I run the command without the "-Q33" I get the following:
fastx_quality_stats: Invalid quality score value (char '#' ord 35 quality value -29) on line 4
I'm eager to try suggestions, so please let me know ! thanks
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